Doc-Alignment

  Inter-genomic and intra-genomic comparisons can help reveal the structural complexity of Cucurbitales genomes. We used V.vinifera as a reference, and by comparing homologous gene locus maps and Ks values between V.vinifera and other Cucurbitales, we could separate orthologous and paralogous genes produced by different polyploidization in the species genomes. We created a hierarchical lists of homologous genes using V.vinifera as a reference.
  The relevant gene ids can be obtained from the Cucurbitales blast and match under the Tools module. This link is Cucurbitales blast and match.

Orthogroup analysis platform
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Select Vvi1 Blo1 Blo2 Bda1 Bda2 Bpe1 Bpe2 Bma1 Bma2 Cmo1 Cmo2 Cma1 Cma2 Car1 Car2 Sed1 Cpe1 Cpe2 Bhi1 Tan1 Cmetu1 Lac1 Hepe1 Mch1 Lcy1 Cla1 Cam1 Cec1 Cco1 Clacu1 Cmu1 Cre1 Cone1 Cone2 Cone3 Cone4 Lsi1 Csa1 Chy1 Cme1 Blo3 Blo4 Bda3 Bda4 Bpe3 Bpe4 Bma3 Bma4 Sed2 Cmo3 Cmo4 Cma3 Cma4 Car3 Car4 Cpe3 Cpe4 Bhi2 Tan2 Cmetu2 Lac2 Hepe2 Mch2 Lcy2 Cla2 Cam2 Cec2 Cco2 Clacu2 Cmu2 Cre2 Lsi2 Csa2 Chy2 Cme2
Vvi5g189 . . . . . . . . . Cmo17g00383 . . . . . . . . . . . . . . Cla06g00399 Cam06g0420 Cec06g0428 Cco06g0428 Clacu06g0407 Cmu06g0407 Cre06g1186 . . . . . . Chy11g01605 . . . . . . . . . . . . . Cma17g00394 . Car17g00365 . . . . . . . . . . . . . . . . Lsi09g01519 . . Cme11g02111
Vvi5g190 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g191 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g192 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cla05g00732 Cam05g0801 Cec05g0809 Cco05g0811 Clacu05g0790 Cmu05g0753 Cre05g0830 . Csa03g01548 Chy06g00784 .
Vvi5g193 . . . . . . . . Cmo08g01267 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda13g00238 . . . . . . . Cma08g01304 . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g194 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bpe13g00758 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g195 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g196 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g197 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g198 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
13 2968627 2970560 + Bda001118.3 Bda13g00238 238
13 14108726 14115058 + Bpe010452.1 Bpe13g00758 758
5 7070184 7072284 - CaPI482276_05g008010.1 Cam05g0801 801
6 6331461 6350346 + CaPI482276_06g004200.1 Cam06g0420 420
17 2326040 2339950 - Carg05572-RA Car17g00365 365
5 6805486 6807595 - CcPI632755_05g008110.1 Cco05g0811 811
6 4697245 4714977 + CcPI632755_06g004280.1 Cco06g0428 428
5 6816198 6818304 - CePI673135_05g008090.1 Cec05g0809 809
6 4840206 4860340 + CePI673135_06g004280.1 Cec06g0428 428
6 5498160 5500341 + Chy6G113120.1 Chy06g00784 784
11 22599378 22612588 - Chy11G201850.1 Chy11g01605 1605
5 6777532 6779632 - ClG42_05g0079000.10 Clacu05g0790 790
6 4869740 4888606 + ClG42_06g0040700.10 Clacu06g0407 407
5 6936092 6939800 - ClCG05G006830.2 Cla05g00732 732
6 4894948 4913414 + ClCG06G004280.1 Cla06g00399 399
8 7893696 7903914 + CmaCh08G013040.1 Cma08g01304 1304
17 2220854 2238323 - CmaCh17G003940.1 Cma17g00394 394
11 28713961 28728067 - MELO3C021240.2.1 Cme11g02111 2111
8 7972020 7985206 + CmoCh08G012670.1 Cmo08g01267 1267
17 2368870 2383591 - CmoCh17G003830.1 Cmo17g00383 383
5 6633080 6635178 - CmPI595203_05g007530.1 Cmu05g0753 753
6 4664963 4683822 + CmPI595203_06g004070.1 Cmu06g0407 407
5 7442966 7445071 - CrPI670011_05g008300.1 Cre05g0830 830
6 5721313 5740233 + CrPI670011_06g011860.1 Cre06g1186 1186
3 11548761 11552129 + CsaV3_3G015480.1 Csa03g01548 1548
9 23296207 23311465 - Lsi09G015190.1 Lsi09g01519 1519
5 1912865 1914014 + Vvi5g189 Vvi5g189 189
5 1914034 1924596 + Vvi5g190 Vvi5g190 190
5 1924622 1925889 + Vvi5g191 Vvi5g191 191
5 1929697 1937783 - Vvi5g192 Vvi5g192 192
5 1938562 1950410 - Vvi5g193 Vvi5g193 193
5 1950533 1953765 + Vvi5g194 Vvi5g194 194
5 1961983 1962270 + Vvi5g195 Vvi5g195 195
5 1962649 1964733 - Vvi5g196 Vvi5g196 196
5 1975298 1976766 - Vvi5g197 Vvi5g197 197
5 1976783 1988796 - Vvi5g198 Vvi5g198 198
       

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